2jri
Solution structure of the Josephin domain of Ataxin-3 in complex with ubiquitin molecule.
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 2jri |
| 沉积日期 deposition_date | 2007-06-27 |
| 结构标题 title | Solution structure of the Josephin domain of Ataxin-3 in complex with ubiquitin molecule. |
| 关键词 keywords | ;di-ubiquitin, Lys48-linked, Josephin domain of ataxin-3, spinocerebellar ataxia type 3 protein, Alternative splicing, Hydrolase, Neurodegeneration, Nucleus, Phosphorylation, Polymorphism, Transcription, Transcription regulation, Triplet repeat expansion, HYDROLASE-SIGNALING PROTEIN COMPLEX ;; HYDROLASE/SIGNALING PROTEIN |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 22.34 Å |
| 回转半径 Rg (电子) rg_electron | 22.01 Å |
| 零角强度 I(0) i0 | 7857690000.00 |
| 分子量 molecular_weight | 762730.0 kDa |
| 排除体积 excluded_volume | 957370 ų |
| 包络体积 envelope_volume | 76596 ų |
| 水化壳体积 shell_volume | 27400 ų |
| 包络直径 envelope_diameter | 77.1 Å |
| 壳层 Rg shell_rg | 30.63 Å |
| 包络 Rg envelope_rg | 23.32 Å |
| 形状 Rg shape_rg | 21.98 Å |
| 总 Rg total_rg | 22.21 Å |
| 总原子数 total_atoms | 107540 |
| 残基数 n_residues | 6680 |
| 球谐函数阶数 n_harmonics | 20 |
| q 范围 q_range | — – 0.5000 Å−1 |
| 数据点数 n_points | 101 |
| 壳层类型 shell_type | directional |
| 溶剂电子密度 solvent_density | 0.3340 e/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 69.8 Å |
| Rg (实空间) rg_real | 22.29 Å |
| Rg 误差 (实空间) rg_real_error | 0.40 Å |
| I(0) (实空间) i0_real | 7.8580e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.0280e+08 |
| Rg (倒空间) rg_reciprocal | 22.30 Å |
| I(0) (倒空间) i0_reciprocal | 7858000000.0000 |
| 解质量估计 total_estimate | 0.9097 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 68.8 Å |
| 偏度 Skewness skewness | 0.237 |
| 峰度 Kurtosis kurtosis | -0.494 |
| 角度范围 angular_range | — – 0.3550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 3325000.0000 |
| 实空间数据点数 n_real_points | 67 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 6 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2jrib_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
| 结构域编号 domain_id | d2jric_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2jriA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 70 — Cathepsin B; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 40 — |
| 结构域编号 domain_id | 2jriA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 10 — S15/NS1, RNA-binding |
| 结构域编号 domain_id | 2jriB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |
| 结构域编号 domain_id | 2jriC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |